Neurology Commons^™

Genetics Of Cerebral Palsy: Diagnosis, Differential Diagnosis, And Beyond, Dae-Hyun Jang, Jaewon Kim, Aloysia Leisanne Schwabe, Timothy Edward Lotze

Faculty, Staff and Students Publications

Cerebral palsy (CP) is the most common motor disability in children, characterized by diverse clinical manifestations and often uncertain etiology, which has spurred increasing interest in genetic diagnostics. This review synthesizes findings from various studies to enhance understanding of CP's genetic underpinnings. The discussion is structured around five key areas: monogenic causes and copy number variants directly linked to CP, differential genetic disorders including atypical CP and mimics, ambiguous genetic influences, co-occurrence with other neurodevelopmental disorders, and polygenic risk factors. Case studies illustrate the clinical application of these genetic insights, underscoring the complexity of diagnosing CP due to the phenotypic …

Increased Neuroinflammation And Compromised Blood Brain Barrier In A Mouse Model Of Autism, Amani S. Ikram, Rekha Jagadapillai, Idil Tuncali, Gregory N. Barnes, Evelyne Gozal

The Cardinal Edge

No abstract provided.

Modeling Antisense Oligonucleotide Therapy In Mecp2 Duplication Syndrome Human Ipsc-Derived Neurons Reveals Gene Expression Programs Responsive To Mecp2 Levels, Sameer S Bajikar, Yehezkel Sztainberg, Alexander J Trostle, Harini P Tirumala, Ying-Wooi Wan, Caroline L Harrop, Jesse D Bengtsson, Claudia M B Carvalho, Davut Pehlivan, Bernhard Suter, Jeffrey L Neul, Zhandong Liu, Paymaan Jafar-Nejad, Frank Rigo, Huda Y Zoghbi

Faculty, Staff and Students Publications

Genomic copy-number variations (CNVs) that can cause neurodevelopmental disorders often encompass many genes, which complicates our understanding of how individual genes within a CNV contribute to pathology. MECP2 duplication syndrome (MDS or MRXSL in OMIM; OMIM#300260) is one such CNV disorder caused by duplications spanning methyl CpG-binding protein 2 (MECP2) and other genes on Xq28. Using an antisense oligonucleotide (ASO) to normalize MECP2 dosage is sufficient to rescue abnormal neurological phenotypes in mouse models overexpressing MECP2 alone, implicating the importance of increased MECP2 dosage within CNVs of Xq28. However, because MDS CNVs span MECP2 and additional genes, we generated human …

An Expansion Of The Phenotype In Individuals With Syncrip-Related Neurodevelopmental Disorder, Tooba Shafiq, Joanna Feng, Lindsay Phillips, Kara Murias, Marcia Ferguson, Kristin Baranano, Alaina Acchione, Patricia Kipkemoi, Collins Kipkoech, Amina Abubakar

Institute for Human Development, East Africa

Disruption of genes within the HNRNP gene family has been observed in neurodevelopmental and neurodegenerative diseases. The HNRNP-Related Neurodevelopmental Disorders (HNRNP-RNDDs), while each unique, have been recently described with similar clinical and molecular features across variation in several genes. However, the phenotypic information on these patients is still lacking. In this case series we aim to describe the phenotypes that are associated with SYNCRIP-Related Neurodevelopmental Disorder (SYNCRIP-RNDD). We describe in depth ten novel individuals and one previously published individual with mostly de novo and predicted damaging variants in SYNCRIP, consistent with a diagnosis of SYNCRIP-RNDD. We also describe previously published …

Removing Lead From The Global Economy, Stephen P. Luby, Jenna E. Forsyth, Zafar Fatmi, Mahbubur Rahman, Jesmin Sultana, Erica L. Plambeck, N Grant Miller, Eran Bendavid, Peter J. Winch, Howard Hu

Community Health Sciences

No abstract provided.

Long-Term Efficacy And Safety Of Cannabidiol In Patients With Tuberous Sclerosis Complex: 3-Year Results From The Cannabidiol Expanded Access Program, Arie Weinstock, E Martina Bebin, Daniel Checketts, Gary D Clark, Jerzy P Szaflarski, Laurie E Seltzer, Elizabeth A Thiele, Farhad Sahebkar

Faculty, Staff and Students Publications

OBJECTIVE: The cannabidiol (CBD) Expanded Access Program provided compassionate access to CBD for patients with treatment-resistant epilepsy, including tuberous sclerosis complex (TSC), at 35 US epilepsy centers. Here, we present the long-term efficacy and safety outcomes for add-on CBD treatment in patients with TSC.

METHODS: Patients received plant-derived, highly purified CBD (Epidiolex® 100 mg/mL, oral solution), increasing from 2 to 10 mg/kg/d to tolerance or maximum of 25-50 mg/kg/d. Efficacy endpoints were percentage change from baseline in median monthly convulsive, focal, and total seizure frequency and ≥ 50%, ≥75%, and 100% responder rates across 12-week visit windows through 144 weeks. …

Acute Changes In Liver Function Tests During Initiation Of Ketogenic Diet, Akshat Katyayan, Anuranjita Nayak, Gloria Diaz-Medina, Maureen Handoko, James John Riviello

Faculty, Staff and Students Publications

BACKGROUND: Ketogenic diet is an effective therapy for patients with medically refractory epilepsy. It is generally well tolerated, with the most common side effects being gastrointestinal. Hepatic toxicity has been described as an uncommon side effect of ketogenic diet, usually with long-term use. However, there are limited data to implicate ketogenic diet in acute liver toxicity.

METHODS AND RESULTS: We analyzed all patients who underwent elective inpatient ketogenic diet initiation at our institution from June 2019 to June 2022. Of the 25 patients reviewed, we found 6 patients who showed acute, asymptomatic changes in liver function tests during initiation, in …

Tau Is Required For Glial Lipid Droplet Formation And Resistance To Neuronal Oxidative Stress, Lindsey D Goodman, Isha Ralhan, Xin Li, Shenzhao Lu, Matthew J Moulton, Ye-Jin Park, Pinghan Zhao, Oguz Kanca, Ziyaneh S Ghaderpour Taleghani, Julie Jacquemyn, Joshua M Shulman, Kanae Ando, Kai Sun, Maria S Ioannou, Hugo J Bellen

Duncan NRI Faculty and Staff Publications

The accumulation of reactive oxygen species (ROS) is a common feature of tauopathies, defined by Tau accumulations in neurons and glia. High ROS in neurons causes lipid production and the export of toxic peroxidated lipids (LPOs). Glia uptake these LPOs and incorporate them into lipid droplets (LDs) for storage and catabolism. We found that overexpressing Tau in glia disrupts LDs in flies and rat neuron-astrocyte co-cultures, sensitizing the glia to toxic, neuronal LPOs. Using a new fly tau loss-of-function allele and RNA-mediated interference, we found that endogenous Tau is required for glial LD formation and protection against neuronal LPOs. Similarly, …

Microglia In Post-Mortem Hippocampal Brain Tissue Of Male And Female Neonates After Hie, Kassandra M. Pulido, Angela N. Viaene, Amelia J. Eisch, Danielle G. Barber

Research Colloquium

Background: Hypoxic-ischemic encephalopathy (HIE) is the second-leading cause of neonatal morbidity and mortality worldwide. There are sex differences in the pathophysiology of HIE, particularly in microglia, which are critical in the immune response. Prior work highlights microglial aggregation in the hippocampus of human infants as a marker for HIE, but it is unknown whether this differs by sex.

Aim: We compare the microglial response in post-mortem hippocampal tissue from male and female neonates diagnosed with HIE vs. Controls who expired from other causes.

Methods: Using a retrospective cohort design, we reviewed medical records of neonates with hippocampal tissue in the …

Distinct Basal Forebrain-Originated Neural Circuits Promote Homoeostatic Feeding And Suppress Hedonic Feeding In Male Mice, Hailan Liu, Jonathan C Bean, Yongxiang Li, Meng Yu, Olivia Z Ginnard, Kristine M Conde, Mengjie Wang, Xing Fang, Hesong Liu, Longlong Tu, Na Yin, Junying Han, Yongjie Yang, Qingchun Tong, Benjamin R Arenkiel, Chunmei Wang, Yang He, Yong Xu

Faculty, Staff and Students Publications

Feeding behaviour is influenced by two primary factors: homoeostatic needs driven by hunger and hedonic desires for pleasure even in the absence of hunger. While efficient homoeostatic feeding is vital for survival, excessive hedonic feeding can lead to adverse consequences such as obesity and metabolic dysregulations. However, the neurobiological mechanisms that orchestrate homoeostatic versus hedonic food consumption remain largely unknown. Here we show that GABAergic proenkephalin (Penk) neurons in the diagonal band of Broca (DBB) of male mice respond to food presentation. We further demonstrate that a subset of DBBPenk neurons that project to the paraventricular nucleus of the hypothalamus …

Self-Harm In Female Youth With Undiagnosed Adhd: Implementing American Academy Of Pediatrics Screening Guidelines, Roselie M. Woodard

Dissertations

Attention deficit hyperactivity disorder (ADHD) is a common neurodevelopmental disorder characterized by inattention, hyperactivity, and impulsivity. If undiagnosed or untreated, ADHD can lead to severe psychosocial issues such as academic failure, substance abuse, unplanned pregnancy, and incarceration. The financial burden in the U.S. from diagnostic errors creates an immense, rising fiscal impact. Early diagnosis and management are crucial to prevent these complications.

Females with ADHD, particularly those with the inattentive subtype, often face diagnostic challenges due to symptom masking and over-compensation. This results in poorer cognitive functioning and self-esteem compared to males with ADHD. ADHD is linked to autonomic nervous …

Bayesian Varying-Effects Vector Autoregressive Models For Inference Of Brain Connectivity Networks And Covariate Effects In Pediatric Traumatic Brain Injury, Yangfan Ren, Nathan Osborne, Christine B Peterson, Dana M Demaster, Linda Ewing-Cobbs, Marina Vannucci

Faculty, Staff and Student Publications

In this article, we develop an analytical approach for estimating brain connectivity networks that accounts for subject heterogeneity. More specifically, we consider a novel extension of a multi-subject Bayesian vector autoregressive model that estimates group-specific directed brain connectivity networks and accounts for the effects of covariates on the network edges. We adopt a flexible approach, allowing for (possibly) nonlinear effects of the covariates on edge strength via a novel Bayesian nonparametric prior that employs a weighted mixture of Gaussian processes. For posterior inference, we achieve computational scalability by implementing a variational Bayes scheme. Our approach enables simultaneous estimation of group-specific …

Expanded-Access Use Of Elamipretide In A Patient With Membrane Protein-Associated Neurodegeneration, Jorge Patino, Anna Haertling Clearman, Lindsey Miller, Mary Kay Koenig

Faculty, Staff and Student Publications

This case report presents a progressively declining 17-year-old patient with membrane protein-associated neurodegeneration who demonstrated symptomatic improvements in her dysarthria, dysphagia, and gait, and objective improvements in her 6-minute walk test and 5 times sit-to-stand test during elamipretide treatment.

Occupational Therapy In Stroke: A Case Study Using The Bobath Frame Of Reference And Task Oriented Approach, Reza Nur Arsyi, Afifah Fadhilah Nursyam, Muhammad Luthfi, Hermito Gidion, Ayleen Alicia Kosasi, Erna Faryza Mohd Poot, Rosilah Wahab, Nur Atiqah Azman

Jurnal Fisioterapi Terapan Indonesia

Stroke is a sudden neurological disorder caused by vascular injury to the brain, leading to significant functional limitations. This case study examines the use of occupational therapy interventions, specifically the Bobath and Task Oriented approaches, for a 43-year-old male with left hemiparesis to enhance independence in motorcycling. The patient experienced various limitations, including vestibular function, range of motion, muscle tone and strength, postural control, and fine motor skills. Using the Ashworth scale and the Canadian Occupational Performance Measure (COPM) for assessment, occupational therapy interventions showed progress in several aspects, although the primary goal has not yet been fully achieved. This …

Terapi Latihan Pada Fase Satu Pasca Operasi Rekonstruksi Ruptur Anterior Cruciate Ligamentum Sinistra, Aunike Arum Meta Wurgani, Irawan Wibisono

Jurnal Fisioterapi Terapan Indonesia

Anterior Cruciate Ligament (ACL) reconstruction is a surgical procedure involving the grafting of the ACL using tendon tissue. This procedure aims to restore knee stability and joint fixation following an ACL injury. Post-ACL reconstruction often leads to complications such as pain, edema, reduced range of motion, and muscle weakness. The physiotherapy program in this case aims to evaluate the effects of physiotherapy interventions, including quadriceps setting, hamstring setting, straight leg raise (SLR), heel slide, ankle pumping, bridging, and prone hang exercises, in reducing edema and pain, as well as improving the range of motion and muscle strength in the knee …

Jump To Box Kombinasi Core Plank Knee To Elbow Terhadap Power Otot Tungkai, Maya Triyanita

Jurnal Fisioterapi Terapan Indonesia

Leg power training is defined as a movement to get the jump in athletes doing the maximum jump smash. Badminton requires leg muscle explosive power because it is the muscle's ability to overcome loads and with a high speed of contraction. This study aims to determine differences in the effect of jump to box training, a combination of core plank knee to elbow on increasing leg power in badminton athletes. This study used an experimental design method with a pre-test and post-test design. The treatment group was given the Jump To Box Combination Core Plank Knee To Elbow exercise. The …

Rigor And Reproducibility In Human Brain Organoid Research: Where We Are And Where We Need To Go, Soraya O Sandoval, Gerarda Cappuccio, Karina Kruth, Sivan Osenberg, Saleh M Khalil, Natasha M Méndez-Albelo, Krishnan Padmanabhan, Daifeng Wang, Mark J Niciu, Anita Bhattacharyya, Jason L Stein, André M M Sousa, Elisa A Waxman, Elizabeth D Buttermore, Dosh Whye, Carissa L Sirois, Cross-Iddrc Human Stem Cell Consortium, Aislinn Williams, Mirjana Maletic-Savatic, Xinyu Zhao

Faculty, Staff and Students Publications

Human brain organoid models have emerged as a promising tool for studying human brain development and function. These models preserve human genetics and recapitulate some aspects of human brain development, while facilitating manipulation in an in vitro setting. Despite their potential to transform biology and medicine, concerns persist about their fidelity. To fully harness their potential, it is imperative to establish reliable analytic methods, ensuring rigor and reproducibility. Here, we review current analytical platforms used to characterize human forebrain cortical organoids, highlight challenges, and propose recommendations for future studies to achieve greater precision and uniformity across laboratories.

Feasibility Of Achieving Nutritional Adequacy In Critically Ill Children With Critical Neurological Illnesses (Cnis)?-A Quaternary Hospital Experience, Marwa Mansour, Nicole Knebusch, Jennifer Daughtry, Thomas P Fogarty, Fong Wilson Lam, Renan A Orellana, Yi-Chen Lai, Jennifer Erklauer, Jorge A Coss-Bu

Faculty, Staff and Students Publications

The literature on the nutritional needs and outcomes of critically ill children is scarce, especially on those with critical neurological illnesses (CNIs). Current evidence shows a lower mortality in patients who achieve two-thirds of their nutritional needs during the first week of pediatric intensive care unit (PICU) admission. We hypothesized that achieving 60% of the recommended dietary intake during the first week of a PICU stay is not feasible in patients with CNI. We designed an observational retrospective cohort study where we included all index admissions to the PICU in our institution of children (1 month to 18 years) with …

Adaptive, Behavioral, And Emotional Outcomes Following Postoperative Pediatric Cerebellar Mutism Syndrome In Survivors Treated For Medulloblastoma, Kimberly P Raghubar, Andrew M Heitzer, Fatema Malbari, Jason Gill, Roy V Sillitoe, Livia Merrill, Johanna Escalante, M Fatih Okcu, Guillermo Aldave, Avner Meoded, Stephen Kralik, Kimberly Davis, Marina Ma, Emily A H Warren, Mark D Mccurdy, Howard L Weiner, William Whitehead, Michael E Scheurer, Lisa Rodriguez, Amy Daigle, Murali Chintagumpala, Lisa S Kahalley

Faculty, Staff and Students Publications

OBJECTIVE: Patients who experience postoperative pediatric cerebellar mutism syndrome (CMS) during treatment for medulloblastoma have long-term deficits in neurocognitive functioning; however, the consequences on functional or adaptive outcomes are unknown. The purpose of the present study was to compare adaptive, behavioral, and emotional functioning between survivors with and those without a history of CMS.

METHODS: The authors examined outcomes in 45 survivors (15 with CMS and 30 without CMS). Comprehensive neuropsychological evaluations, which included parent-report measures of adaptive, behavioral, and emotional functioning, were completed at a median of 2.90 years following craniospinal irradiation.

RESULTS: Adaptive functioning was significantly worse in …

Atp1a3 Disease Spectrum Includes Paroxysmal Weakness And Encephalopathy Not Triggered By Fever, Chetan Immanneni, Daniel Calame, Song Jiao, Lisa T Emrick, Miguel Holmgren, Sho T Yano

Faculty, Staff and Students Publications

BACKGROUND AND OBJECTIVES: Heterozygous pathogenic variants in ATP1A3, which encodes the catalytic alpha subunit of neuronal Na+/K+-ATPase, cause primarily neurologic disorders with widely variable features that can include episodic movement deficits. One distinctive presentation of ATP1A3-related disease is recurrent fever-triggered encephalopathy. This can occur with generalized weakness and/or ataxia and is described in the literature as relapsing encephalopathy with cerebellar ataxia. This syndrome displays genotype-phenotype correlation with variants at p.R756 causing temperature sensitivity of ATP1A3. We report clinical and in vitro functional evidence for a similar phenotype not triggered by fever but associated with protein loss-of-function.

METHODS: We …

Standardization Of Discharge Instructions For Mild Traumatic Brain Injury/Concussion In Children Presenting To Ed: A Qi Project, Niralee K. Rana, Nicole Gerber, Michael Alfonzo, Snezana Osorio, Deborah Levine

Rowan-Virtua Research Day

Background: Mild traumatic brain injuries (mTBI) or concussions account for high rates of emergency department (ED) visits. Concussion diagnoses are used less often in young children leading to a variability in parental education and discharge instructions. Lack of discharge guidance may increase parental anxiety, impact recovery, and increase ED visits.

Objectives: To increase the proportion of ED patients discharged with age-appropriate instructions for mTBI by 50% by June 1, 2024, and to determine the impact age-appropriate instructions have on decreasing parental anxiety.

Methods: This observational time series with planned sequential experimentation is in progress at a Pediatric ED affiliated with …

Abnormality Of Early White Matter Development In Tuberous Sclerosis Complex And Autism Spectrum Disorder: Longitudinal Analysis Of Diffusion Tensor Imaging Measures, Siddharth Srivastava, Fanghan Yang, Anna K Prohl, Peter E Davis, Jamie K Capal, Rajna Filip-Dhima, E Martina Bebin, Darcy A Krueger, Hope Northrup, Joyce Y Wu, Simon K Warfield, Mustafa Sahin, Bo Zhang, Tacern Study Group

Faculty, Staff and Student Publications

Background:

Abnormalities in white matter development may influence development of autism spectrum disorder in tuberous sclerosis complex (TSC). Our goals for this study were as follows: (1) use data from a longitudinal neuroimaging study of tuberous sclerosis complex (TACERN) to develop optimized linear mixed effects models for analyzing longitudinal, repeated diffusion tensor imaging metrics (fractional anisotropy, mean diffusivity) pertaining to select white matter tracts, in relation to positive Autism Diagnostic Observation Schedule–Second Edition classification at 36 months, and (2) perform an exploratory analysis using optimized models applied to all white matter tracts from these data.

Methods:

Eligible participants (3-12 months) …

Childhood Cancer Mutagenesis Caused By Transposase-Derived Pgbd5, Makiko Yamada, Ross R Keller, Rodrigo Lopez Gutierrez, Daniel Cameron, Hiromichi Suzuki, Reeti Sanghrajka, Jake Vaynshteyn, Jeffrey Gerwin, Francesco Maura, William Hooper, Minita Shah, Nicolas Robine, Phillip Demarest, N Sumru Bayin, Luz Jubierre Zapater, Casie Reed, Steven Hébert, Ignas Masilionis, Ronan Chaligne, Nicholas D Socci, Michael D Taylor, Claudia L Kleinman, Alexandra L Joyner, G Praveen Raju, Alex Kentsis

Faculty, Staff and Students Publications

Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling is sufficient to enforce cerebellar granule cell progenitor-like cell states, which exhibit Pgbd5-dependent expression of distinct DNA repair and neurodevelopmental factors. Mouse medulloblastomas expressing Pgbd5 have increased numbers of somatic structural DNA rearrangements, …

Mapping Sca1 Regional Vulnerabilities Reveals Neural And Skeletal Muscle Contributions To Disease, Lisa Duvick, W Michael Southern, Kellie A Benzow, Zoe N Burch, Hillary P Handler, Jason S Mitchell, Hannah Kuivinen, Udaya Gadiparthi, Praseuth Yang, Alyssa Soles, Carrie A Sheeler, Orion Rainwater, Shannah Serres, Erin B Lind, Tessa Nichols-Meade, Yun You, Brennon O'Callaghan, Huda Y Zoghbi, Marija Cvetanovic, Vanessa C Wheeler, James M Ervasti, Michael D Koob, Harry T Orr

Duncan NRI Faculty and Staff Publications

Spinocerebellar ataxia type 1 (SCA1) is a fatal neurodegenerative disease caused by an expanded polyglutamine tract in the widely expressed ataxin-1 (ATXN1) protein. To elucidate anatomical regions and cell types that underlie mutant ATXN1-induced disease phenotypes, we developed a floxed conditional knockin mouse (f-ATXN1146Q/2Q) with mouse Atxn1 coding exons replaced by human ATXN1 exons encoding 146 glutamines. f-ATXN1146Q/2Q mice manifested SCA1-like phenotypes including motor and cognitive deficits, wasting, and decreased survival. Central nervous system (CNS) contributions to disease were revealed using f-ATXN1146Q/2Q;Nestin-Cre mice, which showed improved rotarod, open field, and Barnes maze performance by 6-12 weeks of age. In contrast, …

A Structured, Journal-Led Peer-Review Mentoring Program Enhances Peer Review Training, Ariel Maia Lyons-Warren, Whitley W Aamodt, Kathleen M Pieper, Roy E Strowd

Faculty, Staff and Students Publications

BACKGROUND: Peer review is essential to the advancement of knowledge. However, training on how to conduct peer review is limited, unorganized, and not well studied. Thus, we sought to determine if a structured mentored peer-review program improved peer review training as measured by multiple quantitative and qualitative assessments.

METHODS: This pre-post intervention study enrolled 55 mentees across 5 cohorts from 2020 to 2023. Each cohort completed pre-program evaluations, participated in 2 mentored reviews, and completed post-program evaluations over 6 months. Mentors and mentees completed pre-program demographic and review experience questionnaires. Outcome measures included (1) total and sub-scores on the modified …

The Utility Of Interventional Anesthesia, Kylie Daguio, Kiley Jackson, Samantha Boever, Andrew Chang, James Keane, Leonard B. Goldstein

SOMA Faculty Publications

no abstract

Quantification And Visualization Of Cis-Regulatory Dynamics In Single-Cell Multi-Omics Data With Treasmo, Chaozhong Liu, Linhua Wang, Zhandong Liu

Faculty, Staff and Students Publications

Recent advances in single-cell multi-omics technologies have provided unprecedented insights into regulatory processes. We introduce TREASMO, a versatile Python package designed to quantify and visualize transcriptional regulatory dynamics in single-cell multi-omics datasets. TREASMO has four modules, spanning data preparation, correlation quantification, downstream analysis and visualization, enabling comprehensive dataset exploration. By introducing a novel single-cell gene-peak correlation strength index, TREASMO facilitates accurate identification of regulatory changes at single-cell resolution. Validation on a hematopoietic stem and progenitor cell dataset showcases TREASMO's capacity in quantifying the gene-peak correlation strength at the single-cell level, identifying regulatory markers and discovering temporal regulatory patterns along the …

Heterozygous Map3k20 Variants Cause Ectodermal Dysplasia, Craniosynostosis, Sensorineural Hearing Loss, And Limb Anomalies, Daniel Brooks, Elizabeth Burke, Sukyeong Lee, Tanya N Eble, Melanie O'Leary, Ikeoluwa Osei-Owusu, Heidi L Rehm, Shweta U Dhar, Lisa Emrick, David Bick, Michelle Nehrebecky, Ellen Macnamara, Dídac Casas-Alba, Judith Armstrong, Carolina Prat, Antonio F Martínez-Monseny, Francesc Palau, Pengfei Liu, David Adams, Undiagnosed Diseases Network, Seema Lalani, Jill A Rosenfeld, Lindsay C Burrage

Faculty, Staff and Students Publications

Biallelic pathogenic variants in MAP3K20, which encodes a mitogen-activated protein kinase, are a rare cause of split-hand foot malformation (SHFM), hearing loss, and nail abnormalities or congenital myopathy. However, heterozygous variants in this gene have not been definitively associated with a phenotype. Here, we describe the phenotypic spectrum associated with heterozygous de novo variants in the linker region between the kinase domain and leucine zipper domain of MAP3K20. We report five individuals with diverse clinical features, including craniosynostosis, limb anomalies, sensorineural hearing loss, and ectodermal dysplasia-like phenotypes who have heterozygous de novo variants in this specific region of the gene. …

Polyaminer-Bulk Is A Deep Learning-Based Algorithm That Decodes Alternative Polyadenylation Dynamics From Bulk Rna-Seq Data, Venkata Soumith Jonnakuti, Eric J Wagner, Mirjana Maletić-Savatić, Zhandong Liu, Hari Krishna Yalamanchili

Faculty, Staff and Students Publications

Alternative polyadenylation (APA) is a key post-transcriptional regulatory mechanism; yet, its regulation and impact on human diseases remain understudied. Existing bulk RNA sequencing (RNA-seq)-based APA methods predominantly rely on predefined annotations, severely impacting their ability to decode novel tissue- and disease-specific APA changes. Furthermore, they only account for the most proximal and distal cleavage and polyadenylation sites (C/PASs). Deconvoluting overlapping C/PASs and the inherent noisy 3' UTR coverage in bulk RNA-seq data pose additional challenges. To overcome these limitations, we introduce PolyAMiner-Bulk, an attention-based deep learning algorithm that accurately recapitulates C/PAS sequence grammar, resolves overlapping C/PASs, captures non-proximal-to-distal APA changes, …

Cpsf3 Inhibition Blocks Pancreatic Cancer Cell Proliferation Through Disruption Of Core Histone Mrna Processing, Abdulrahman A Alahmari, Aditi H Chaubey, Venkata S Jonnakuti, Arwen A Tisdale, Carla D Schwarz, Abigail C Cornwell, Kathryn E Maraszek, Emily J Paterson, Minsuh Kim, Swati Venkat, Eduardo Cortes Gomez, Jianmin Wang, Katerina V Gurova, Hari Krishna Yalamanchili, Michael E Feigin

Faculty, Staff and Students Publications

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target cleavage and polyadenylation specificity factor 3 (CPSF3), the 3′ endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated with poor prognosis. CPSF3 knockdown blocks PDAC cell proliferation and colony formation in vitro and tumor growth in vivo. Chemical inhibition of CPSF3 by the small molecule JTE-607 also attenuates PDAC cell proliferation and colony formation, while it has no effect on cell proliferation …